good morning Eric…
there will be lots of debate on this topic since there are so many *right* ways to do this….
i export a QT mov file from AE using the animation codec (the codec — if you use one — will be dependent upon your content) and then use squeeze to get the final swf from there…. i’m not sure what version of squeeze you are using but there should be no issue with using non-standard video sizes and maintain your pixel aspect….
you could also export an uncompressed avi file from AE and then use squeeze on that…
and i dont know your content but 12.5 frames per second will look choppy…
and you said “flash movie for the web”… have you thought about using flv format instead of swf?
and unfortunately there are no “best” settings… experimentation IS needed on each product from my humble perspective…